How I perform fpkm on a file containing the raw reads of two samples and each sample have three replicates? I want to do the analysis in R.
Question: How to perform FPKM on raw reads in R
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manish20072013 • 10 wrote:
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modified 23 months ago
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Ahmed Alhendi • 50
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3.7 years ago by
manish20072013 • 10
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Istvan Albert ♦♦ 86k wrote:
See the blog post "What the FPKM" by Harold Pimentel that also provides R code:
https://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units/
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Ahmed Alhendi • 50 wrote:
Try countToFPKM package. This package provides an easy to use function to convert the read count matrix into FPKM values normalised by library size and feature effective length. It also provides the user with a reliable function to generate FPKM heatmap plot of the highly variable features in RNA-Seq dataset.; following the equation:
.
The fpkm()
function requires three inputs to return FPKM as numeric matrix normalized by library size and feature length:
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